Methods of quality control using single-nucleotide polymorphisms in pre-implantation genetic screening

ABSTRACT

The present invention provides methods for validating results of a pre-implantation genetic screen. Methods of the invention increase the efficacy of the common PGS assay FAST-SeqS by taking advantage of single-nucleotide polymorphisms (SNPs) generated from the assay to confirm copy number calls, detect errors, identify samples, and recognize and identify sources of contamination. Methods of the invention increase the reliability of a PGS result, thereby making embryo selection more precise and improving outcomes of in vitro fertilization.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of and priority to U.S. ProvisionalPatent Application Ser. No. 62/103,802, filed Jan. 15, 2015, thecontents of which are incorporated herein by reference in theirentirety.

FIELD OF THE INVENTION

The invention generally relates to pre-natal genetic testing, andspecifically to using SNPs to validate copy number, to identify theorigin of a sample, or to detect contamination in the sample.

BACKGROUND

When a woman has difficulty becoming pregnant, she may turn to in vitrofertilization (IVF). IVF involves removing one or more ova from awoman's ovary, fertilizing it and growing it in a laboratory, andimplanting it into the uterus of the patient who desires to becomepregnant. However, numerous difficulties with IVF exist. Successfulpregnancies are only achieved in approximately 29% of cycles, and onlyabout 22% result in live births.

One way to increase the chance of a full term pregnancy is to undergopre-implantation genetic screening (PGS). PGS involves assessing thechromosome copy number of embryos to screen out those that are aneuploidand are thus not good candidates for implantation. Aneuploidy is acondition in which the number of chromosomes is not an exact multiple ofthe haploid number (23 in humans). Most aneuploidies, such as trisomyand monosomy, are lethal to the fetus. Others, such as trisomy 21 (Downsyndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patausyndrome), cause congenital defects, growth deficiencies, andintellectual disabilities in the child. PGS aims to avoid those problemsby screening out aneuploid embryos from implantation.

Existing methods of PGS involve analyzing read counts of DNA sequenceson each chromosome to detect differences in copy number indicative ofaneuploidy. However, analytical errors can lead to false positiveaneuploidy calls. Additionally, read count alone cannot distinguishcertain altered copy number states, including triploidy, haploidy, anduniparental disomy.

SUMMARY

The present invention provides methods of validating the result of apre-implantation genetic screen. Methods of the invention increase theefficacy of the PGS assay, FAST-SeqS, by taking advantage ofsingle-nucleotide polymorphisms (SNPs) generated from the assay toconfirm copy number calls, detect errors, identify samples, andrecognize and identify sources of contamination. Methods of theinvention increase the reliability of a PGS result, thereby makingembryo selection more precise and improving outcomes of in vitrofertilization.

In embodiments, the invention provides a method for validating aputative chromosome copy number in a genomic sample using SNPs capturedby FAST-SeqS method. The SNPs are sequenced to determine allele fractionacross various loci. The allele fraction can be compared to thechromosome copy numbers determined by FAST-SeqS method to determine ifthose copy numbers are valid. For example, a copy number indicatingmonosomy would be invalidated by the detection of a heterozygous SNP orSNPs on a particular chromosome. Alternatively, an allele fractionshowing loss of heterozygosity may prove that a copy number indicatingdiploidy is actually haploid. Various other permutations are describedbelow.

In other embodiments of the invention, the SNPs amplified and sequencedin the FAST-SeqS method are utilized to generate unique DNAfingerprints, which help identify samples. DNA fingerprinting is usefulfor determining whether two embryos are siblings, whether two samplesare from the same embryo, and whether the correct embryo was selectedand implanted. It also is useful for confirming proper labeling andidentification of samples during testing, thereby reducing the incidenceof human error affecting IVF results.

In another embodiment, SNPs can be used to detect human contamination ina sample by calling out allele fractions or other characteristics of theSNPs that fail to conform to an expected distribution. When samplecontamination has occurred, the allelic pattern of the SNPs can be usedto back out the fingerprint of the contaminating sample and identify thesource of contamination.

In embodiments, the SNP-based approach to calling chromosome copynumbers, DNA fingerprinting, and contamination detection can be used forother applications beyond PGS. The methods described herein are usefulfor cancer screening, forensics, paternity testing, screening forgenetic disorders, monitoring cancer treatments, and many other uses aswould be known in the art.

In certain aspects, the invention provides a method for validating aputative chromosome copy number in a genomic sample. The method involvesobtaining sequencing reads from a genomic sample amplified by FAST-SeqS;enumerating read counts from the sequencing reads; calculating putativechromosome copy numbers of the genomic sample based on the read counts;obtaining allele fractions for SNPs in a region covered by thesequencing reads; and comparing the allele fractions to the putativechromosome copy numbers to validate the putative chromosome copynumbers.

In some embodiments of the method, the genomic sample is biopsied froman embryo. In some embodiments, the genomic sample comprises circulatingcell-free fetal DNA, amniotic fluid, chorionic villus, fetal cells inmaternal blood, trophoblasts, umbilical cord blood, tumor biopsy, orcirculating tumor DNA.

In embodiments, an allele fraction that is inconsistent with theputative chromosome copy number invalidates the putative chromosome copynumber. A putative chromosome copy number of 1 may indicate monosomy; aputative chromosome copy number of 2 may indicate disomy; and a putativechromosome copy number of 3 may indicate trisomy. In embodiments, anallele fraction may indicate a genomic locus is homozygous or that agenomic locus is heterozygous. An allele fraction or set of allelefractions of 100% may indicate monosomy, whereas an allele fraction orset of allele fractions of 50% may indicate disomy. An allele fractionor set of allele fractions between 10% and 40% or between 60 and 90% mayindicate trisomy or tetrasomy. A putative chromosome copy number of 2combined with allele fractions inconsistent with diploidy may indicatetriploidy, haploidy, or isodisomic uniparental disomy.

In some embodiments, the method further involves identifying allelefractions that deviate from an expected allele fraction by more than athreshold amount. The threshold may be, for example, 10% or 20%. Inembodiments, the method may involve diagnosing trisomy 21, trisomy 18,trisomy 13, or another aneuploidy condition.

In other aspects of the invention, a method is provided for validating aputative chromosome copy number in a genomic sample. The method involvesobtaining putative chromosome copy numbers for a genomic sample, thecopy numbers calculated from sequence read counts of FAST-SeqS-amplifiedDNA; obtaining allele fractions of SNPs in the genomic sample, the SNPssequenced from FAST-SeqS-amplified DNA; comparing the allele fractionsto the putative chromosome copy numbers; and determining whether theputative chromosome copy numbers are consistent with the allelefractions.

In certain embodiments, the genomic sample is biopsied from an embryo.The genomic sample may include circulating cell-free fetal DNA, amnioticfluid, chorionic villus, fetal cells in maternal blood, trophoblasts,umbilical cord blood, tumor biopsy, or circulating tumor DNA.

In embodiments, an allele fraction that is inconsistent with theputative chromosome copy number invalidates the putative chromosome copynumber. A putative chromosome copy number of 1 may indicate monosomy; aputative chromosome copy number of 2 may indicate disomy; and a putativechromosome copy number of 3 may indicate trisomy. In embodiments, anallele fraction may indicate a genomic locus is homozygous or that agenomic locus is heterozygous. An allele fraction or set of allelefractions of 100% may indicate monosomy, whereas an allele fraction orset of allele fractions of 50% may indicate disomy. An allele fractionor set of allele fractions between 10% and 40% or between 60 and 90% mayindicate trisomy or tetrasomy. A putative chromosome copy number of 2combined with allele fractions inconsistent with diploidy may indicatetriploidy, haploidy, or isodisomic uniparental disomy.

In some embodiments, the method further involves identifying allelefractions that deviate from an expected allele fraction by more than athreshold amount. The threshold may be, for example, 10% or 20%. Inembodiments, the method may involve diagnosing trisomy 21, trisomy 18,trisomy 13, or another aneuploidy condition.

In other aspects, the invention provides a method for determining adegree of relatedness between two genomic samples. The method involvesobtaining sequence reads from a first genomic sample and a secondgenomic sample amplified by FAST-SeqS; determining genotype calls at aplurality of SNP loci on the samples, based on the sequence reads;generating a DNA fingerprint for each sample based on the genotypecalls; and comparing the DNA fingerprint of the first genomic sample tothe DNA fingerprint of the second genomic sample to determine a degreeof relatedness between the two samples. In embodiments, the firstgenomic sample includes a biopsy from an embryo or circulating cell-freefetal DNA.

In some embodiments of the method, generating a DNA fingerprint involvesassigning a numerical score to each SNP locus and concatenating thenumerical scores into a string, wherein determining a degree ofrelatedness involves calculating a distance metric between the DNAfingerprints. DNA fingerprinting includes numerical scores that identifyat least two of the following states: heterozygous reference,heterozygous alternate, and homozygous. The method may further involvedetermining phylogeny based on the calculated distance metric. A degreeof relatedness greater than a threshold value may indicate that thesamples are identical, whereas a degree of relatedness below a thresholdvalue may indicate the samples are from different sources. Inembodiments, the first genomic sample includes DNA from an embryo andthe second genomic sample is biopsied from a fetus putatively derivedfrom the embryo. In other embodiments, the first genomic samplecomprises DNA from an embryo and the second genomic sample comprises DNAfrom a sibling embryo.

Another aspect of the invention provides a method for detectingcontamination in a sample. The method involves obtaining sequence readsfrom a genomic sample amplified by FAST-SeqS; identifying, based on thesequence reads, a characteristic of SNPs present in the genomic sample;comparing the characteristic to an expected characteristic for thegenomic sample; and determining, based on the comparison, whethercontamination has occurred.

In embodiments, the characteristic includes genotype calls, allelefractions, or a quantity of non-homozygous SNPs. The genomic sample mayinclude a biopsy from an embryo or circulating cell-free fetal DNA. Incertain embodiments of the method, the second determining step is basedon whether the comparison reveals the characteristic of SNPs exceeds athreshold. The expected characteristic may be based on a characteristicof a known diploid sample.

The method may further involve determining a DNA fingerprint of acontaminant based on the comparison and identifying a source ofcontamination based on the DNA fingerprint.

In other aspects, the invention provides a method for determiningchromosome copy number. The method involves obtaining allele fractionsfor SNPs sequenced by FAST-SeqS and determining chromosome copy numberbased on the allele fractions.

In some embodiments of the method, the genomic sample is biopsied froman embryo. In some embodiments, the genomic sample comprises circulatingcell-free fetal DNA, amniotic fluid, chorionic villus, fetal cells inmaternal blood, trophoblasts, umbilical cord blood, tumor biopsy, orcirculating tumor DNA.

In embodiments, an allele fraction may indicate a genomic locus ishomozygous or that a genomic locus is heterozygous. An allele fractionor set of allele fractions of 100% may indicate monosomy, whereas anallele fraction or set of allele fractions of 50% may indicate disomy.An allele fraction or set of allele fractions between 10% and 40% orbetween 60 and 90% may indicate trisomy or tetrasomy.

In some embodiments, the method further involves identifying allelefractions that deviate from an expected allele fraction by more than athreshold amount. The threshold may be, for example, 10% or 20%. Inembodiments, the method may involve diagnosing trisomy 21, trisomy 18,trisomy 13, or another aneuploidy condition.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a flowchart of a method for making copy number calls anddetecting errors.

FIG. 2 shows a flowchart of a method for DNA fingerprinting.

FIG. 3 shows a flowchart of a method for detecting contamination.

DETAILED DESCRIPTION

The present disclosure is generally directed to validating the resultsof pre-implantation genetic screening (PGS). One key objective common toPGS and multiple other genetic tests (e.g. cancer tumor sequencing andpre-natal screening) is to accurately determine the copy number of eachchromosome. Such an accurate calling of chromosome copy number shouldenable both the identification of aneuploidy as well as the presence ofan unexpected integral multiple of the haploid chromosome count. Typesof aneuploidy include monosomy (one copy of a chromosome), trisomy(three copies of a chromosome), and tetrasomy (four copies of achromosome) and common examples of unexpected integral multiples of thehalploid chromosome count include triploidy (three full sets ofchromosomes), tetrasomy (four full sets of chromosomes), haploidy (oneset of chromosomes), and isodisomic uniparental disomy (two sets ofchromosomes, both from one parent).

Methods of PGS known in the art, such as FAST-SeqS, are useful fordetecting chromosomal aneuploidies and other chromosome countabnormalities. But those methods are still subject to errors (falsepositives and false negatives) and contamination of samples.

Single-nucleotide polymorphisms (SNPs) sequenced from an embryo grown invitro or from circulating cell-free fetal DNA (ccffDNA) obtained from apregnant woman, for example, can be used to provide insights aboutaneuploidies, other chromosome count abnormalities, and contamination.The SNPs for use with the present invention can come from DNA capturedby massively parallel sequencing techniques such as FAST-SeqS.

The FAST-SeqS method involves capturing fragments from all chromosomesin a sample with a single primer pair. Using a single primer pairstreamlines the PGS process. Prior techniques required preparation ofwhole genome libraries, which involved many complicated and technicallychallenging steps including, whole genome amplification, DNAfragmentation, end-repair, 5′-phosphorylation, addition of terminal dAnucleotides to 3′ ends, ligation to adapters, PCR amplification, severalpurification steps, sequencing, and chromosome copy number calling.FAST-SeqS avoids many of those steps by using a single primer pair and asmall but effective number of DNA fragments to be assessed, rather thanthe whole genome. See International Patent Application Publication No.WO 2013148496; and Kinde et al., 2012, “FAST-SeqS: A Simple andEfficient Method for the Detection of Aneuploidy by Massively ParallelSequencing,” PLOS ONE 7(7):e41162, the entirety of which is incorporatedherein by reference.

Single-nucleotide polymorphisms (SNPs) captured and sequenced by theFAST-SeqS method can be used for a number of applications in PGS. Thepresent disclosure provides uses for the sequenced SNPs including copynumber calling and error detection, DNA fingerprinting, and detection ofhuman contamination. As would be understood by a person of skill in theart, the SNP-based approaches described herein can be used for manyother genetic screening applications beyond PGS. The methods describedherein are useful for cancer screening, forensics, paternity testing,screening for genetic disorders, monitoring cancer treatments, and more.

a. Copy Number Calling and Error Detection

FAST-SeqS detects aneuploidies using chromosome copy numbers obtainedfrom sequence reads across a chromosome of interest. However, usingsequence reads alone can lead to analytical errors that yield falsepositive aneuploidy calls (particularly for monosomy, trisomy, andtetrasomy) and ambiguous results with respect to other chromosome countabnormalities (e.g., triploidy, haploidy, and uniparental disomy).

For example, variable sequence read depths or other analyticalirregularities may contribute to a false call of monosomy when the readcount data indicate that a particular chromosome has only one copy whencompared with the sequence reads of other chromosomes in a sample. Usingread counts alone is subject to inaccuracies. However, according to thepresent disclosure, a monosomy result can be confirmed by assaying SNPsof the chromosome in question.

FIG. 1 shows a method 100 for validating a putative chromosome copynumber call. The method 100 includes a first step 105 of obtainingsequence reads from a genomic sample amplified by FAST-SeqS. The samplemay comprise embryonic tissue, ccffDNA, chorionic villus tissue,amniotic fluid, fetal cells in maternal blood, trophoblasts, umbilicalcord blood, or any other sample type known in the art for use withprenatal diagnosis. The sample may also comprise tumor DNA orcirculating tumor DNA. A second step 109 comprises enumerating readcounts from the sequence reads. Then in step 113 putative chromosomecopy numbers are calculated based on the read counts. Optionally, aperson practicing methods of the invention can begin by obtainingputative chromosome copy numbers for a genomic sample, wherein the copynumbers have been calculated from sequence read counts ofFAST-SeqS-amplified DNA performed by another individual. Once putativechromosome copy numbers are obtained, the method continues in step 117with obtaining allele fractions for SNPs captured by FAST-SeqS sequencereads.

An allele fraction is the proportion of a particular allele at a locusof interest. It may be expressed as a percentage. For example, ahomozygous locus could be said to have an allele fraction of 100%,whereas a diploid locus that is heterozygous could be said to have anallele fraction of 50%. When measuring allele fraction some margin oferror may be expected, and so a measured allele fraction of 47%, forexample, may still be called a heterozygous diploid locus. However, asdiscussed in greater detail below, allele fractions that deviatesignificantly from 100% or 50% may be indicative of aneuploidy.

The allele fractions and the putative chromosome copy numbers arecompared in step 121 to validate the putative chromosome copy numbers.Depending on what type of aneuploidy (or euploidy) is indicated by theputative chromosome copy number data, the validation step may compriselooking at different comparison metrics between the two sets of data.Generally, when an observed allele fraction is inconstant with theputative chromosome copy number, that result invalidates the putativechromosome copy number.

In one embodiment, a researcher may want to validate a monosomy callindicated by the putative chromosome copy number (i.e., copy number of1). To detect a false monosomy call in a sample on a chromosome that isactually diploid, a researcher may look for the presence ofnon-homozygous genotype calls along the chromosome. An allele fractionof 100% would be consistent with monosomy, but the presence ofheterozygous SNPs (presence of two alleles) at any genomic loci wouldreveal a copy number of at least 2. A copy number of 2 would indicate atleast disomy. In such a case, the monosomy call based on read countswould prove to be an erroneous result. On the other hand, if the SNPsalong the chromosome of interest revealed an apparent loss ofheterozygosity, the monosomy call would be confirmed.

Using similar methods, a false trisomy or tetrasomy call can be detectedas well. In a sample where read counts indicate more than two copies ofa chromosome (i.e., trisomy or tetrasomy), a researcher can examineallele fractions of heterozygous SNP calls along that chromosome. In thecase of a false call, heterozygous call allele fractions would not bestatistically different from expectation for a diploid sample, i.e.approximately 50% for each allele. The presence of approximately 50% ofeach heterozygous allele would indicate that there are in fact twocopies of the chromosome. A tolerance threshold can be used, wherein ifan allele frequency is between, for example 45% and 55%, it isconsidered to be present in two copies. Alternatively, the tolerancethreshold can be 40% to 60%.

However, if the allele fractions of heterozygous calls were shiftedsignificantly from that expected for the diploid case, that would beindicative of a true trisomy or tetrasomy if observed in the presence ofan elevated copy number measurement based on read count. If the allelefrequencies fall outside the tolerance threshold (for example, if oneallele is present at 25% and the other is present at 75%), theresearcher can conclude aneuploidy exists.

Triploidy, haploidy, and isodisomic uniparental disomy present differentanalytical problems for the researcher. Based on read count alone, thoseabnormalities would appear to be diploid. That is because read countrelies on the relative number of reads between chromosomes to identifyoutliers. Using SNPs, however, can reveal the correct ploidy level ofthe sample. For example, to detect triploidy (i.e., having 3 times thehaploid number of chromosomes, or 3n) in a sample whose read countsyield a putative copy number of 2 for all autosomes, the sample can beassayed for the number of heterozygous SNP calls and, separately, theallele fractions of the heterozygous SNP calls in the sample. If eitherthe number of heterozygous SNPs differs from the expectation for adiploid sample, or if the allele fraction distribution of heterozygousSNP calls differs from an expected allele fraction distribution (i.e.,differs significantly from 50%), it can be inferred that the sample istriploid even though the read-based copy number measurement isindicative of diploidy.

Similarly, one can detect haploidy or isodisomic uniparental disomy(iUPD) in a sample determined to be diploid by read counts alone. Thegenotypes of a plurality (or preferably all) of callable known SNP locican be assessed. If the genotypes of the plurality of SNP sites exhibitsa loss of heterozygosity, one can infer the presence of haploidy or iUPDin the sample even though the read-based copy number measurement isindicative of diploidy.

Using the methods described above can confirm or refute a copy numberdetermined by FAST-SeqS alone. The methods allow for more effectiveidentification of chromosomal anomalies such as trisomy 21, trisomy 18,and trisomy 13.

b. DNA Fingerprinting

DNA fingerprinting (also known as DNA profiling or DNA typing) is atechnique well known in the art, which can be used to identify anindividual using their DNA. DNA fingerprinting relies on highly variablesequences that differ from one person to the next.

The present disclosure provides methods of using genotype calls of SNPsfrom FAST-SeqS amplified DNA to generate DNA fingerprints to identifysamples. The method involves performing FAST-SeqS on the sample andgenerating genotype calls across multiple loci. As shown in FIG. 2, amethod 200 of for determining a degree of relatedness using DNAfingerprinting may comprise a first step 205 of obtaining sequence readsfrom two genomic samples amplified by FAST-SeqS. A sample may comprisean embryo biopsy, ccffDNA, amniotic fluid, and the like. Alternativelyit could comprise saliva, blood, a buccal swab, or any other bodilycellular sample, as would be understood by those skilled in the artdepending on the particular comparison to be performed. Next in step209, genotype calls are determined at a plurality of SNP loci on thesamples, based on the sequence reads. A DNA fingerprint is generated instep 213 for each sample based on the genotype calls. The genotype callscan be assigned a digital identifier or a numerical score andconcatenated into a string. For example, the digital identifiers can be0, 1, and 2, corresponding to homozygous reference, homozygousalternate, and heterozygous genotypes, respectively. Alternatively, thedigital identifier could be condensed in such a manner that 0 indicatesthe presence of only the reference allele and 1 indicates the presenceof the non-reference allele (homozygous non-reference or heterozygous).

The concatenated string of genotype calls or digital identifiersconstitutes the DNA fingerprint, and can be compared to the DNAfingerprint of another sample, as shown in step 217, to determine thedegree of relatedness or identity. Samples may be determined to beidentical if they meet some threshold degree relatedness. Methods fordetermining a degree of relatedness are known in the art and may includeperforming clustering on the basis of a distance metric to inferrelatedness.

A fingerprint assigned to a sample can serve as the basis of comparisonto fingerprints from other samples to determine the degree ofrelatedness between them. The fingerprints can determine if two samplesare unrelated, related, or identical. In the context of PGS, thosefingerprints can be used to determine or rule out that a sample swap hasoccurred. Sample swaps can occur due to human error, either by theclinic performing the IVF or by the laboratory analyzing the biopsiedtissue.

DNA fingerprinting can also be used to determine phylogenicrelationships between samples, including confirming paternity. Thesesamples can be embryo biopsies for PGS, or can be other sample types,such as ccffDNA in maternal blood, donor DNA in allograft recipients,blood or saliva samples from individuals seeking to learn about ancestryor relatedness, and biological samples for forensic applications.

In the case of determining whether a sample swap has occurred duringPGS, all embryos from a given patient should exhibit a degree ofrelatedness equivalent to that among siblings. Any embryo from such apatient which does not exhibit a similar level of relatedness cantherefore be identified as a swap. Similarly, if a sample of biologicalfluid or tissue is obtained from the mother, FAST-SeqS can be performedon that sample to determine the fingerprint of the mother. Using thisinformation, it is possible to identify a gross mislabeling of allembryos from a given IVF procedure by determining their relatedness tothe fingerprint derived from her sample.

In addition, it is possible to compare the FAST-SeqS fingerprint of atested embryo before implantation to the fingerprint of a fetus, child,or product of conception supposedly derived from the embryo. That way,one could check to ensure that the chosen embryo is indeed the one thatwas transferred. The procedure would be done in the same manner as notedabove, except rather than comparing DNA fingerprints of two embryosamples to each other, the fingerprint of an embryo would be compared tothat of the alternative sample type with the expectation that thefingerprints would be identical if the correct embryo was indeedutilized.

c. Detection of Human Contamination

Human contamination in a sample being analyzed by the FAST-SeqS methodcan also be identified using SNPs. As would be recognized by a personskilled in the art, allele fractions for homozygous and heterozygouscalls should conform to a specific expected distribution. If thedistribution of allele fractions for any given sample deviates from thatexpectation, it can be inferred that sample contamination has occurred.It may even be possible to back out the actual fingerprint of thecontaminating sample, based on the particular shift for each locus.Accordingly, one can identify the source of contamination.

Additionally, the number of heterozygous SNPs can be used to evaluatewhether contamination exists. If the number of heterozygous loci isparticularly large for a sample, multiple samples may have beensimultaneously amplified. The number of heterozygous loci is consideredlarge when compared to the numbers empirically observed for samplesknown not to be contaminated.

FIG. 3 shows a method 300 for detecting contamination in a sample inaccordance with the present disclosure. The method 300 includes thefirst step 305 of obtaining sequence reads from a genomic sampleamplified by FAST-SeqS technology. The sample may comprise embryonictissue, ccffDNA, chorionic villus tissue, amniotic fluid, fetal cells inmaternal blood, trophoblasts, umbilical cord blood, or any other sampletype known in the art for use with prenatal diagnosis. The sample mayalso comprise tumor DNA or circulating tumor DNA. Next, in step 309, acharacteristic of SNPs in the genomic sample is identified from thesequence reads. The characteristic can be genotype calls across multipleSNP loci. It can also be allele fractions at one or more SNP loci.Alternatively, the characteristic can be a quantity of non-homozygousSNPs in the sample. In some embodiments, only one of thosecharacteristics is used. In other embodiments, multiple are used. Usingmultiple characteristics may increase the reliability of the result.Other similar characteristics that are known in the art can also beused.

The method 300 includes a step 313 of comparing the characteristicidentified in step 309 to an expected characteristic for anon-contaminated genomic sample. For example, a practitioner of themethod 300 may make a comparison to the expected genotype calls for aknown diploid sample or set of diploid samples. The expectedcharacteristic can be any of the characteristics described above thatwere identified in step 309. The comparison helps determine in step 313whether the sample is an outlier and therefore contamination hasoccurred. That determination can be based on whether the comparisonshows that the characteristic measured in the SNPs exceeds somethreshold.

Optionally, if a sample is determined to be an outlier, the method 300may comprise deducing the fingerprint of the contaminating moiety by“backing out” its genotype based on the direction of shift away fromexpectation for each SNP or other polymorphic locus.

Incorporation by Reference

References and citations to other documents, such as patents, patentapplications, patent publications, journals, books, papers, webcontents, have been made throughout this disclosure. All such documentsare hereby incorporated herein by reference in their entirety for allpurposes.

Equivalents

Various modifications of the invention and many further embodimentsthereof, in addition to those shown and described herein, will becomeapparent to those skilled in the art from the full contents of thisdocument, including references to the scientific and patent literaturecited herein. The subject matter herein contains important information,exemplification and guidance that can be adapted to the practice of thisinvention in its various embodiments and equivalents thereof.

What is claimed is:
 1. A method for validating a putative chromosomecopy number in a genomic sample, the method comprising: obtainingsequencing reads from a genomic sample amplified by FAST-SeqS;enumerating read counts from the sequencing reads; calculating putativechromosome copy numbers of the genomic sample based on the read counts;obtaining allele fractions for SNPs in a region covered by thesequencing reads; and comparing the allele fractions to the putativechromosome copy numbers to validate the putative chromosome copynumbers.
 2. The method of claim 1, wherein the genomic sample isbiopsied from an embryo.
 3. The method of claim 1, wherein the genomicsample comprises circulating cell-free fetal DNA, amniotic fluid,chorionic villus, fetal cells in maternal blood, trophoblasts, umbilicalcord blood, tumor biopsy, or circulating tumor DNA.
 4. The method ofclaim 1, wherein an allele fraction that is inconsistent with theputative chromosome copy number invalidates the putative chromosome copynumber.
 5. The method of claim 1, wherein a putative chromosome copynumber of 1 indicates monosomy; wherein a putative chromosome copynumber of 2 indicates disomy; and wherein a putative chromosome copynumber of 3 indicates trisomy.
 6. The method of claim 1, wherein anallele fraction indicates a genomic locus is homozygous or heterozygous.7. The method of claim 1, wherein an allele fraction or set of allelefractions of 100% indicates monosomy; wherein an allele fraction or setof allele fractions of 50% indicates disomy; and wherein an allelefraction or set of allele fractions between 10% and 40% or between 60and 90% indicates trisomy or tetrasomy.
 8. The method of claim 1,wherein a putative chromosome copy number of 2 combined with allelefractions inconsistent with diploidy indicates triploidy, haploidy, orisodisomic uniparental disomy.
 9. The method of claim 1, furthercomprising identifying allele fractions that deviate from an expectedallele fraction by more than a threshold amount.
 10. The method of claim1, further comprising diagnosing trisomy 21, trisomy 18, trisomy 13, oranother aneuploidy condition.
 11. A method for validating a putativechromosome copy number in a genomic sample, the method comprising:obtaining putative chromosome copy numbers for a genomic sample, thecopy numbers calculated from sequence read counts of FAST-SeqS-amplifiedDNA; obtaining allele fractions of SNPs in the genomic sample, the SNPssequenced from FAST-SeqS-amplified DNA; comparing the allele fractionsto the putative chromosome copy numbers; and determining whether theputative chromosome copy numbers are consistent with the allelefractions.
 12. The method of claim 11, wherein the genomic sample isbiopsied from an embryo.
 13. The method of claim 11, wherein the genomicsample comprises circulating cell-free fetal DNA, amniotic fluid,chorionic villus, fetal cells in maternal blood, trophoblasts, umbilicalcord blood, tumor biopsy, or circulating tumor DNA.
 14. The method ofclaim 11, wherein an allele fraction or set of allele fractions that isinconsistent with the putative chromosome copy number invalidates theputative chromosome copy number.
 15. The method of claim 11, wherein aputative chromosome copy number of 1 indicates monosomy; wherein aputative chromosome copy number of 2 indicates disomy; and wherein aputative chromosome copy number of 3 indicates trisomy.
 16. The methodof claim 11, wherein an allele fraction indicates a genomic locus ishomozygous or heterozygous.
 17. The method of claim 11, wherein anallele fraction or set of allele fractions of 100% indicates monosomy;wherein an allele fraction or set of allele fractions of 50% indicatesdisomy; and wherein an allele fraction or set of allele fractionsbetween 10% and 40% or between 60 and 90% indicates trisomy ortetrasomy.
 18. The method of claim 11, wherein a putative chromosomecopy number of 2 combined with an allele fraction or allele fractionsinconsistent with diploidy indicates triploidy, haploidy, or isodisomicuniparental disomy.
 19. The method of claim 11, further comprisingidentifying allele fractions that deviate from an expected allelefraction by more than a threshold amount.
 20. The method of claim 11,further comprising diagnosing trisomy 21, trisomy 18, trisomy 13, oranother aneuploidy condition.